A troop in Texas prays that the Boy Scouts of America would maintain their policy of excluding gay scouts and scoutmasters. Photograph: Adam Sacasa/AP

Sometimes, a moment serves as a marker of both how far we've come as a society and how far we have yet to go. The questionnaire concerning its anti-gay policy that the Boy Scouts of America sent out to its 1.1m members days ago is one such moment.

The questionnaire is intended to assess members' attitudes toward the Scouts' current policy of excluding gay people, as well as their likely response to any future change in policy. One question reads:

"David, a Boy Scout, believes that homosexuality is wrong. His troop is chartered to a church where the doctrine of that faith also teaches that homosexuality is wrong. Steve, an openly gay youth, applies to become a member. Is it acceptable or unacceptable for this troop to deny Steve membership in their troop?"

The good news here is that the BSA is raising the issue. The bad news is that they assume that we should take for granted that there are many people like David: people who continue to see same-sex attractions as a moral failure and who are evidently entitled to use their religion as a cover for their bigotry. Substitute "interracial marriage" or "Catholicism" for "homosexuality" in the above question, and you will get a measure of how much room we have to grow as a society.

There is a certain irony, of course, in using a questionnaire to establish individual rights. After all, the point of rights is to protect individuals and minorities against the tyranny of a majority. The irony is compounded by the fact that the Boy Scouts claims to be an organization dedicated to moral principles.

However, let's give the Scouts the benefit of the doubt by assuming that they will use the results of this survey not to make their decision concerning the rights of those with same-sex attractions, but to understand and anticipate the impact of possible policy changes on the organization in the future.

Maybe the strongest marker of the Zeitgeist in the Boy Scouts questionnaire has to do with the role of religion in it. On the one hand, the survey implicitly recognizes that religion is the primary motivator and justifier of its discriminatory policies with respect to gay people. While homophobic people may be either religious or non-religious, we must recognize that the organized political efforts to deprive LGBT people of rights in America have come overwhelmingly from religious conservatives. (This is a point that even some LGBT activist groups are loath to acknowledge – perhaps for tactical reasons.)

On the other hand, the questionnaire, like much of the coverage surrounding it, is silent about the role of religion in shaping the Boy Scout's discriminatory policies in another area, one that is distinct from and yet intimately connected with its bigotry toward gay people.

Adult leaders in the Boy Scouts must sign a Declaration of Religious Principles, and Scouts must take an oath "to do my duty to God". Both adults and children can and have been excluded from the organization for lack of belief in a supreme being (or beings). Neil Polzin, who had been in the Scouts for nearly two decades, says he was fired in 2009 from his job as an aquatics director at a Boy Scout camp and told to "sever any ties" with the organization after his superiors found out about his non-belief.

Even the irreligion of parents can be a basis for excluding children from the group. In 1991, 12-year-old scout Matthew Schottmiller was not allowed to renew his membership after it was learned that he was raised in a non-theist household. His mother, Margaret Downey – who was rearing her son to be a freethinker – filed suit. But the supreme court ruled in 2000 that, as a private organization, the Boy Scouts is free to decide their own membership criteria.

The supreme court is right – at least, in some sense. In the US, private groups can and should be allowed to control their membership without legal interference. On the other hand, private groups aren't necessarily entitled to a congressional charter, regular support from government agencies, and endorsement from government officials – all of which the Boy Scouts do enjoy.

The silence about religiously motivated discrimination against the non-religious – especially in comparison with the noise about religiously motivated discrimination against gay people – reflects the fact that discrimination against non-believers remains an acceptable form of bigotry in America. A Gallup poll from 2011 showed that only 54% of Americans say they would be willing to vote for an atheist for president – making atheists less popular than Muslims (58%) and gay people (68%).

Among the many factors that might explain this broad aversion to perceived religious deviance is a widespread belief about belief. Taken as a whole – setting aside "David" and his "church" – Americans are increasingly tending toward the view that same-sex attractions are not a moral choice but a matter of fate, some combination of genes and environmental or historical factors for which the individual should not be held accountable.

We persist, however, in seeing religious belief in religious terms – that is, as simply a matter of moral choice. God has given us his Word, the common thinking goes, and we can choose to believe it or not, just as we can choose what color of socks to wear or whether to rob a bank today.

But belief isn't simply a matter of choice. Some people seem born to believe, or are born in contexts where nonbelief is highly unlikely. Others come into the world with no interest in religion at all, or come to the realization that the religious beliefs to which they were exposed simply do not make sense to them. Most non-believers I know don't have the option of believing in a deity or deities any more than they have the option of believing that grasshoppers can speak.

"The opinions and belief of men depend not on their own will, but follow involuntarily the evidence proposed to their minds," said Thomas Jefferson, and he was basically right. He also knew that the evidence proposed to the mind might very well lead some people to atheism. "Question with boldness even the existence of a god," he advised his nephew, Peter Carr, in a letter of 1787:

"Do not be frightened from this inquiry by any fear of its consequences. If it ends in a belief that there is no god, you will find incitements to virtue in the comfort and pleasantness you feel in its exercise, and the love of others which it will procure you."

The Girl Scouts, by the way, removed God from their oath in 1993. America's founders had no God in the oath they prescribed in 1787. In fact, they explicitly stated:

"No religious test shall ever be required as a qualification to any office or public trust under the United States."

Maybe the Boy Scouts, who like to say that they stand for all that is good and right in America, should look to the example set by the United States constitution.